Examples with Dosage org.hl7.fhir.r5.model.Dosage used on opensource projects

Example 21 with Dosage

use of org.hl7.fhir.r5.model.Dosage in project synthea by synthetichealth.

the class FhirR4 method medicationRequest.

/**
 * Map the given Medication to a FHIR MedicationRequest resource, and add it to the given Bundle.
 *
 * @param person         The person being prescribed medication
 * @param personEntry    The Entry for the Person
 * @param bundle         Bundle to add the Medication to
 * @param encounterEntry Current Encounter entry
 * @param medication     The Medication
 * @return The added Entry
 */
private static BundleEntryComponent medicationRequest(Person person, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Medication medication) {
    MedicationRequest medicationResource = new MedicationRequest();
    if (USE_US_CORE_IG) {
        Meta meta = new Meta();
        meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest");
        medicationResource.setMeta(meta);
    } else if (USE_SHR_EXTENSIONS) {
        medicationResource.addExtension().setUrl(SHR_EXT + "shr-base-ActionCode-extension").setValue(PRESCRIPTION_OF_DRUG_CC);
        medicationResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-medication-MedicationRequested"));
        Extension requestedContext = new Extension();
        requestedContext.setUrl(SHR_EXT + "shr-action-RequestedContext-extension");
        requestedContext.addExtension(SHR_EXT + "shr-action-Status-extension", new CodeType("completed"));
        requestedContext.addExtension(SHR_EXT + "shr-action-RequestIntent-extension", new CodeType("original-order"));
        medicationResource.addExtension(requestedContext);
    }
    medicationResource.setSubject(new Reference(personEntry.getFullUrl()));
    medicationResource.setEncounter(new Reference(encounterEntry.getFullUrl()));
    Code code = medication.codes.get(0);
    String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI;
    medicationResource.setMedication(mapCodeToCodeableConcept(code, system));
    if (USE_US_CORE_IG && medication.administration) {
        // Occasionally, rather than use medication codes, we want to use a Medication
        // Resource. We only want to do this when we use US Core, to make sure we
        // sometimes produce a resource for the us-core-medication profile, and the
        // 'administration' flag is an arbitrary way to decide without flipping a coin.
        org.hl7.fhir.r4.model.Medication drugResource = new org.hl7.fhir.r4.model.Medication();
        Meta meta = new Meta();
        meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication");
        drugResource.setMeta(meta);
        drugResource.setCode(mapCodeToCodeableConcept(code, system));
        drugResource.setStatus(MedicationStatus.ACTIVE);
        BundleEntryComponent drugEntry = newEntry(person, bundle, drugResource);
        medicationResource.setMedication(new Reference(drugEntry.getFullUrl()));
    }
    medicationResource.setAuthoredOn(new Date(medication.start));
    medicationResource.setIntent(MedicationRequestIntent.ORDER);
    org.hl7.fhir.r4.model.Encounter encounter = (org.hl7.fhir.r4.model.Encounter) encounterEntry.getResource();
    medicationResource.setRequester(encounter.getParticipantFirstRep().getIndividual());
    if (medication.stop != 0L) {
        medicationResource.setStatus(MedicationRequestStatus.STOPPED);
    } else {
        medicationResource.setStatus(MedicationRequestStatus.ACTIVE);
    }
    if (!medication.reasons.isEmpty()) {
        // Only one element in list
        Code reason = medication.reasons.get(0);
        for (BundleEntryComponent entry : bundle.getEntry()) {
            if (entry.getResource().fhirType().equals("Condition")) {
                Condition condition = (Condition) entry.getResource();
                // Only one element in list
                Coding coding = condition.getCode().getCoding().get(0);
                if (reason.code.equals(coding.getCode())) {
                    medicationResource.addReasonReference().setReference(entry.getFullUrl());
                }
            }
        }
    }
    if (medication.prescriptionDetails != null) {
        JsonObject rxInfo = medication.prescriptionDetails;
        Dosage dosage = new Dosage();
        dosage.setSequence(1);
        // as_needed is true if present
        dosage.setAsNeeded(new BooleanType(rxInfo.has("as_needed")));
        if (rxInfo.has("as_needed")) {
            dosage.setText("Take as needed.");
        }
        // as_needed is false
        if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
            Timing timing = new Timing();
            TimingRepeatComponent timingRepeatComponent = new TimingRepeatComponent();
            timingRepeatComponent.setFrequency(rxInfo.get("dosage").getAsJsonObject().get("frequency").getAsInt());
            timingRepeatComponent.setPeriod(rxInfo.get("dosage").getAsJsonObject().get("period").getAsDouble());
            timingRepeatComponent.setPeriodUnit(convertUcumCode(rxInfo.get("dosage").getAsJsonObject().get("unit").getAsString()));
            timing.setRepeat(timingRepeatComponent);
            dosage.setTiming(timing);
            Quantity dose = new SimpleQuantity().setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
            DosageDoseAndRateComponent dosageDetails = new DosageDoseAndRateComponent();
            dosageDetails.setType(new CodeableConcept().addCoding(new Coding().setCode(DoseRateType.ORDERED.toCode()).setSystem(DoseRateType.ORDERED.getSystem()).setDisplay(DoseRateType.ORDERED.getDisplay())));
            dosageDetails.setDose(dose);
            List<DosageDoseAndRateComponent> details = new ArrayList<DosageDoseAndRateComponent>();
            details.add(dosageDetails);
            dosage.setDoseAndRate(details);
            if (rxInfo.has("instructions")) {
                String text = "";
                for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
                    JsonObject instruction = instructionElement.getAsJsonObject();
                    Code instructionCode = new Code(SNOMED_URI, instruction.get("code").getAsString(), instruction.get("display").getAsString());
                    text += instructionCode.display + "\n";
                    dosage.addAdditionalInstruction(mapCodeToCodeableConcept(instructionCode, SNOMED_URI));
                }
                dosage.setText(text);
            }
        }
        List<Dosage> dosageInstruction = new ArrayList<Dosage>();
        dosageInstruction.add(dosage);
        medicationResource.setDosageInstruction(dosageInstruction);
    }
    BundleEntryComponent medicationEntry = newEntry(person, bundle, medicationResource);
    // create new claim for medication
    medicationClaim(person, personEntry, bundle, encounterEntry, medication.claim, medicationEntry);
    // Create new administration for medication, if needed
    if (medication.administration) {
        medicationAdministration(person, personEntry, bundle, encounterEntry, medication, medicationResource);
    }
    return medicationEntry;
}

Example 22 with Dosage

use of org.hl7.fhir.r5.model.Dosage in project synthea by synthetichealth.

the class FhirStu3 method medicationAdministration.

/**
 * Add a MedicationAdministration if needed for the given medication.
 *
 * @param rand Source of randomness to use when generating ids etc
 * @param personEntry       The Entry for the Person
 * @param bundle            Bundle to add the MedicationAdministration to
 * @param encounterEntry    Current Encounter entry
 * @param medication        The Medication
 * @param medicationRequest The related medicationRequest
 * @return The added Entry
 */
private static BundleEntryComponent medicationAdministration(RandomNumberGenerator rand, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Medication medication, MedicationRequest medicationRequest) {
    MedicationAdministration medicationResource = new MedicationAdministration();
    medicationResource.setSubject(new Reference(personEntry.getFullUrl()));
    medicationResource.setContext(new Reference(encounterEntry.getFullUrl()));
    Code code = medication.codes.get(0);
    String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI;
    medicationResource.setMedication(mapCodeToCodeableConcept(code, system));
    medicationResource.setEffective(new DateTimeType(new Date(medication.start)));
    medicationResource.setStatus(MedicationAdministrationStatus.fromCode("completed"));
    if (medication.prescriptionDetails != null) {
        JsonObject rxInfo = medication.prescriptionDetails;
        MedicationAdministrationDosageComponent dosage = new MedicationAdministrationDosageComponent();
        // as_needed is true if present
        if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
            Quantity dose = new SimpleQuantity().setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
            dosage.setDose((SimpleQuantity) dose);
            if (rxInfo.has("instructions")) {
                for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
                    JsonObject instruction = instructionElement.getAsJsonObject();
                    dosage.setText(instruction.get("display").getAsString());
                }
            }
        }
        medicationResource.setDosage(dosage);
    }
    if (!medication.reasons.isEmpty()) {
        // Only one element in list
        Code reason = medication.reasons.get(0);
        for (BundleEntryComponent entry : bundle.getEntry()) {
            if (entry.getResource().fhirType().equals("Condition")) {
                Condition condition = (Condition) entry.getResource();
                // Only one element in list
                Coding coding = condition.getCode().getCoding().get(0);
                if (reason.code.equals(coding.getCode())) {
                    medicationResource.addReasonReference().setReference(entry.getFullUrl());
                }
            }
        }
    }
    BundleEntryComponent medicationAdminEntry = newEntry(rand, bundle, medicationResource);
    return medicationAdminEntry;
}

Example 23 with Dosage

use of org.hl7.fhir.r5.model.Dosage in project synthea by synthetichealth.

the class FhirStu3 method medication.

/**
 * Map the given Medication to a FHIR MedicationRequest resource, and add it to the given Bundle.
 *
 * @param rand Source of randomness to use when generating ids etc
 * @param personEntry The Entry for the Person
 * @param bundle Bundle to add the Medication to
 * @param encounterEntry Current Encounter entry
 * @param medication The Medication
 * @return The added Entry
 */
private static BundleEntryComponent medication(RandomNumberGenerator rand, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Medication medication) {
    MedicationRequest medicationResource = new MedicationRequest();
    medicationResource.setSubject(new Reference(personEntry.getFullUrl()));
    medicationResource.setContext(new Reference(encounterEntry.getFullUrl()));
    Code code = medication.codes.get(0);
    String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI;
    medicationResource.setMedication(mapCodeToCodeableConcept(code, system));
    medicationResource.setAuthoredOn(new Date(medication.start));
    medicationResource.setIntent(MedicationRequestIntent.ORDER);
    org.hl7.fhir.dstu3.model.Encounter encounter = (org.hl7.fhir.dstu3.model.Encounter) encounterEntry.getResource();
    MedicationRequestRequesterComponent requester = new MedicationRequestRequesterComponent();
    requester.setAgent(encounter.getParticipantFirstRep().getIndividual());
    requester.setOnBehalfOf(encounter.getServiceProvider());
    medicationResource.setRequester(requester);
    if (medication.stop != 0L) {
        medicationResource.setStatus(MedicationRequestStatus.STOPPED);
    } else {
        medicationResource.setStatus(MedicationRequestStatus.ACTIVE);
    }
    if (!medication.reasons.isEmpty()) {
        // Only one element in list
        Code reason = medication.reasons.get(0);
        for (BundleEntryComponent entry : bundle.getEntry()) {
            if (entry.getResource().fhirType().equals("Condition")) {
                Condition condition = (Condition) entry.getResource();
                // Only one element in list
                Coding coding = condition.getCode().getCoding().get(0);
                if (reason.code.equals(coding.getCode())) {
                    medicationResource.addReasonReference().setReference(entry.getFullUrl());
                }
            }
        }
    }
    if (medication.prescriptionDetails != null) {
        JsonObject rxInfo = medication.prescriptionDetails;
        Dosage dosage = new Dosage();
        dosage.setSequence(1);
        // as_needed is true if present
        dosage.setAsNeeded(new BooleanType(rxInfo.has("as_needed")));
        // as_needed is true if present
        if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
            Timing timing = new Timing();
            TimingRepeatComponent timingRepeatComponent = new TimingRepeatComponent();
            timingRepeatComponent.setFrequency(rxInfo.get("dosage").getAsJsonObject().get("frequency").getAsInt());
            timingRepeatComponent.setPeriod(rxInfo.get("dosage").getAsJsonObject().get("period").getAsDouble());
            timingRepeatComponent.setPeriodUnit(convertUcumCode(rxInfo.get("dosage").getAsJsonObject().get("unit").getAsString()));
            timing.setRepeat(timingRepeatComponent);
            dosage.setTiming(timing);
            Quantity dose = new SimpleQuantity().setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
            dosage.setDose(dose);
            if (rxInfo.has("instructions")) {
                for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
                    JsonObject instruction = instructionElement.getAsJsonObject();
                    Code instructionCode = new Code(SNOMED_URI, instruction.get("code").getAsString(), instruction.get("display").getAsString());
                    dosage.addAdditionalInstruction(mapCodeToCodeableConcept(instructionCode, SNOMED_URI));
                }
            }
        }
        List<Dosage> dosageInstruction = new ArrayList<Dosage>();
        dosageInstruction.add(dosage);
        medicationResource.setDosageInstruction(dosageInstruction);
    }
    if (USE_SHR_EXTENSIONS) {
        medicationResource.addExtension().setUrl(SHR_EXT + "shr-base-ActionCode-extension").setValue(PRESCRIPTION_OF_DRUG_CC);
        medicationResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-medication-MedicationRequested"));
        // required fields for this profile are status, action-RequestedContext-extension,
        // medication[x]subject, authoredOn, requester
        Extension requestedContext = new Extension();
        requestedContext.setUrl(SHR_EXT + "shr-action-RequestedContext-extension");
        requestedContext.addExtension(SHR_EXT + "shr-action-Status-extension", new CodeType("completed"));
        requestedContext.addExtension(SHR_EXT + "shr-action-RequestIntent-extension", new CodeType("original-order"));
        medicationResource.addExtension(requestedContext);
    }
    BundleEntryComponent medicationEntry = newEntry(rand, bundle, medicationResource);
    // create new claim for medication
    medicationClaim(rand, personEntry, bundle, encounterEntry, medication.claim, medicationEntry);
    // Create new administration for medication, if needed
    if (medication.administration) {
        medicationAdministration(rand, personEntry, bundle, encounterEntry, medication, medicationResource);
    }
    return medicationEntry;
}

Example 24 with Dosage

use of org.hl7.fhir.r5.model.Dosage in project cqf-ruler by DBCG.

the class ActivityDefinitionApplyProvider method resolveProcedureRequest.

private ProcedureRequest resolveProcedureRequest(ActivityDefinition activityDefinition, String patientId, String practitionerId, String organizationId) throws ActivityDefinitionApplyException {
    // status, intent, code, and subject are required
    ProcedureRequest procedureRequest = new ProcedureRequest();
    procedureRequest.setStatus(ProcedureRequest.ProcedureRequestStatus.DRAFT);
    procedureRequest.setIntent(ProcedureRequest.ProcedureRequestIntent.PROPOSAL);
    String patientReferenceString = patientId;
    URI patientIdAsUri = URI.create(patientReferenceString);
    if (!patientIdAsUri.isAbsolute() && patientIdAsUri.getFragment() == null && !patientReferenceString.startsWith("Patient/")) {
        patientReferenceString = "Patient/" + patientId;
    }
    procedureRequest.setSubject(new Reference(patientReferenceString));
    if (practitionerId != null) {
        procedureRequest.setRequester(new ProcedureRequest.ProcedureRequestRequesterComponent().setAgent(new Reference(practitionerId)));
    } else if (organizationId != null) {
        procedureRequest.setRequester(new ProcedureRequest.ProcedureRequestRequesterComponent().setAgent(new Reference(organizationId)));
    }
    if (activityDefinition.hasExtension()) {
        procedureRequest.setExtension(activityDefinition.getExtension());
    }
    if (activityDefinition.hasCode()) {
        procedureRequest.setCode(activityDefinition.getCode());
    } else // code can be set as a dynamicValue
    if (!activityDefinition.hasCode() && !activityDefinition.hasDynamicValue()) {
        throw new ActivityDefinitionApplyException("Missing required code property");
    }
    if (activityDefinition.hasBodySite()) {
        procedureRequest.setBodySite(activityDefinition.getBodySite());
    }
    if (activityDefinition.hasProduct()) {
        throw new ActivityDefinitionApplyException("Product does not map to " + activityDefinition.getKind());
    }
    if (activityDefinition.hasDosage()) {
        throw new ActivityDefinitionApplyException("Dosage does not map to " + activityDefinition.getKind());
    }
    return procedureRequest;
}

Example 25 with Dosage

use of org.hl7.fhir.r5.model.Dosage in project hl7v2-fhir-converter by LinuxForHealth.

the class FHIRConverterTest method test_dosage_output.

@Test
void test_dosage_output() throws IOException {
    String hl7message = "MSH|^~\\&|MyEMR|DE-000001| |CAIRLO|20160701123030-0700||VXU^V04^VXU_V04|CA0001|P|2.6|||ER|AL|||||Z22^CDCPHINVS|DE-000001\r" + "PID|1||PA123456^^^MYEMR^MR||JONES^GEORGE^M^JR^^^L|MILLER^MARTHA^G^^^^M|20140227|M||2106-3^WHITE^CDCREC|1234 W FIRST ST^^BEVERLY HILLS^CA^90210^^H||^PRN^PH^^^555^5555555||ENG^English^HL70296|||||||2186-5^ not Hispanic or Latino^CDCREC||Y|2\r" + "ORC|RE||197023^CMC|||||||^Clark^Dave||1234567890^Smith^Janet^^^^^^NPPES^L^^^NPI^^^^^^^^MD\r" + "RXA|0|1|20140730||08^HEPB-PEDIATRIC/ADOLESCENT^CVX|.5|mL^mL^UCUM||00^NEW IMMUNIZATION RECORD^NIP001|1234567890^Smith^Janet^^^^^^NPPES^^^^NPI^^^^^^^^MD |^^^DE-000001||||0039F|20200531|MSD^MERCK^MVX|||CP|A";
    String json = ftv.convert(hl7message, OPTIONS);
    FHIRContext context = new FHIRContext();
    IBaseResource bundleResource = context.getParser().parseResource(json);
    assertThat(bundleResource).isNotNull();
    Bundle b = (Bundle) bundleResource;
    List<BundleEntryComponent> e = b.getEntry();
    List<Resource> immunization = e.stream().filter(v -> ResourceType.Immunization == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(immunization).hasSize(1);
    String s = context.getParser().encodeResourceToString(immunization.get(0));
    Class<? extends IBaseResource> klass = Immunization.class;
    Immunization expectDoseQuantity = (Immunization) context.getParser().parseResource(klass, s);
    assertThat(expectDoseQuantity.hasDoseQuantity()).isTrue();
    Quantity dosage = expectDoseQuantity.getDoseQuantity();
    BigDecimal value = dosage.getValue();
    String unit = dosage.getUnit();
    assertThat(value).isEqualTo(BigDecimal.valueOf(.5));
    assertThat(unit).isEqualTo("mL");
}